. Author manuscript; available in PMC: 2018 Jun 15.

Published in final edited form as: J Comput Chem. 2017 Feb 4;38(16):1308–1320. doi: 10.1002/jcc.24691

Table 3.

Transmembrane helix dimer geometries. Crossing angles of pVNVV , GpA, EphA1, and Bnip3 helix dimers from experiments, explicit simulations, and implicit HDGBv3 and HDGBvdW models. A negative sign refers to a right-handed orientation. For the experimental results, the average crossing angles of the NMR structures of 1AFO⁸⁷ for GpA, 2J5D⁸⁸ for Bnip3 and 2K1L⁸⁹ and 2K1L⁸⁹ for EphA1 were calculated.

TM Helix Dimer System	Experiment	Explicit	HDGBv3	HDGBvdW
pVNVV	N/A	~22°	~22°	~22°
GpA	−40.2°⁸⁷	−42°¹⁰¹	39.7° (85%) −48.6° (15%)	40.9° (84%) −48.5° (16%)
Bnip3	−36.39°⁸⁸	−27°, −28°, −35°, 52°⁹⁷	−40.4° (97%) 33.7° (3%)	−39.5°
EphA1	−51.22°⁸⁹ −36.36°⁸⁹	45°⁹⁹ −40°, 20°⁹⁸	−45.2° (53%) 18.5° (47%)	−34.3° (57%) −8.9° (20%) 19.3° (23%)